Question: Known SNPs for rice for Base recalibration using GATK
0
gravatar for nbhardwaj
4.4 years ago by
nbhardwaj130
United States
nbhardwaj130 wrote:

Hi,

I am analyzing rice samples for SNP detection using GATK, and for the base recalibration, I need a set of known sites for rice. For human that is usually dbsnp141.vcf available at the DBSNP ftp site (for human):
 
I was wondering if I could the VCF files for rice (rice_4530  in the same list, Oryza Sativa, which is the rice species that I am analyzing)
 
 
Can I use the VCF file in the link above as the know sites (or gold standards)? Are there additional VCFs out there that I can use?
Thanks.
 
sequencing snp • 2.3k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.4 years ago by nbhardwaj130

This should work and should be good enough. Base recalibration is not going to bring any drastic difference in the results unless your sequencing data is real bad. 

ADD REPLYlink written 4.4 years ago by Ashutosh Pandey11k

This link does not contain anything.

ftp://ftp.ncbi.nih.gov/snp/organisms/rice_4530/VCF/

Where can I find known rice snps (indica and japonica, both)

ADD REPLYlink written 7 months ago by deepti1rao20
1
gravatar for Coryza
4.4 years ago by
Coryza380
Netherlands
Coryza380 wrote:

From the University of Sydney (http://sydney.edu.au/engineering/it/research/conversazione_2009/wangt.pdf):

"Oryza sativa spp.Indica and Oryza 
sativa spp.Japonica EST data sets were 
downloaded from National Centre for 
Biotechnology Information dbEST (Mar -
2009). These datasets contain 106,532 
and 833,672 ESTs, respectively. The 
Single Nucleotide Polymorphism 
database (dbSNP) was downloaded 
from NCBI (rice_4530) for data 
verification."

rice_4530: Oryza sativa, rice_4536: Oryza nivara

 

So my best guess is that it would fit fine for your dataset.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Coryza380

Hi

Am also working on rice genome. Can i use snps from the below database to perform base recalibration?

http://www.oryzasnp.org/_download.zul/Nipponbare

ADD REPLYlink written 2.4 years ago by sukesh141130
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